Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- 1 Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA;
- 2 EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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↵3 These authors contributed equally to this work.
Abstract
Pairwise whole-genome alignment involves the creation of a homology map, capable of performing a near complete transformation of one genome into another. For multiple genomes this problem is generalized to finding a set of consistent homology maps for converting each genome in the set of aligned genomes into any of the others. The problem can be divided into two principal stages. First, the partitioning of the input genomes into a set of colinear segments, a process which essentially deals with the complex processes of rearrangement. Second, the generation of a base pair level alignment map for each colinear segment. We have developed a new genome-wide segmentation program, Enredo, which produces colinear segments from extant genomes handling rearrangements, including duplications. We have then applied the new alignment program Pecan, which makes the consistency alignment methodology practical at a large scale, to create a new set of genome-wide mammalian alignments. We test both Enredo and Pecan using novel and existing assessment analyses that incorporate both real biological data and simulations, and show that both independently and in combination they outperform existing programs. Alignments from our pipeline are publicly available within the Ensembl genome browser.
Footnotes
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↵4 Corresponding authors.
↵4 E-mail benedict{at}soe.ucsc.edu; fax (831) 459-1809.
↵4 E-mail birney{at}ebi.ac.uk; fax +44-(0)1223-494-468.
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[Supplemental material is available online at www.genome.org. Enredo and Pecan are freely available at http://www.ebi.ac.uk/~jherrero/downloads/enredo/ and http://www.ebi.ac.uk/~bjp/pecan/, respectively.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.076554.108.
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- Received January 24, 2008.
- Accepted September 9, 2008.
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Freely available online through the Genome Research Open Access option.
- Copyright © 2008, Cold Spring Harbor Laboratory Press